A stepper motor develops the most torque when forced one full step away from the commanded position. If you make it deviate more than that, it will lose steps (always in multiples of four full steps). Regardless of microstepping, the motor will give the same torque when forced one full step away from wherever you want it to be. If you force it half of a full step, it will apply about 71% of the maximum torque toward where you told it to go. If you force it only a quarter of a step, it will apply 38% of full torque. And so on: if it's already there, in the commanded position, it will generate no torque at all. It follows that a stepper motor moving against the load is always a little bit off from the theoretical position; how much depends on load, but it's up to one full step at maximum load.
Now, if you want to increase precision, you may try to increase microstepping. This improves the resolution (you can command the position with a much finer increment), but it does not improve how accurately the stepper follows the commanded position. It's still the same one full step away from it at the same maximum load. If you want the accuracy to increase in the same proportion as the resolution -- and this is the unstated constraint -- you limit yourself to a smaller deviation than one full step. The only way to do that is to decrease the load: to 71% if you want to double the accuracy, to 38% if you want to quadruple it, and so on.
So the only way microstepping reduces torque is if you're talking about torque per microstep (meaning the torque developed when the motor deviates one microstep from the commanded position), which is a very specific measure. You still get the full torque if it deviates one full step, and that's still the maximum you can go before you lose steps. For most practical purposes, in a machine like this, it's the latter that counts -- maximum torque before you lose steps -- and that stays the same. The extra positioning resolution does not hurt anything, even if it does not translate into increased accuracy; it actually helps, because it reduces a specific type of resonance that can cause lost steps.